Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Micro-PVM"
graph_weight
## [1] "0.5"

Session information

gc()
##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4165351 222.5   10243768 547.1         NA 10243768 547.1
## Vcells 8928651  68.2   29538339 225.4      65536 29518146 225.3
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5